SMTL ID : 6rmd.1

Structure of ATP bound Plasmodium falciparum IMP-nucleotidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-mer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: E.164, E.236, F.349, K.362, L.388, H.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.164, A:E.164, A:E.236 EDO.2: 3 residues within 4Å: Chain A: P.15, Y.16 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.16 EDO.4: 2 residues within 4Å: Chain B: R.13 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.13 EDO.5: 6 residues within 4Å: Chain C: E.164, E.236, F.349, K.362, L.388, H.389 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.164, C:E.236 EDO.6: 3 residues within 4Å: Chain C: P.15, Y.16 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.16 EDO.8: 2 residues within 4Å: Chain D: R.13 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.13

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 10 residues within 4Å: Chain B: Y.71, K.74, Y.75, H.92, N.95, L.96, Q.360, E.361, A.364, C.365 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:H.92, B:N.95, B:L.96 Salt bridges: B:K.74, B:K.74, B:K.74 pi-Stacking: B:H.92, B:H.92 ATP.7: 10 residues within 4Å: Chain D: Y.71, K.74, Y.75, H.92, N.95, L.96, Q.360, E.361, A.364, C.365 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.75, D:H.92, D:N.95, D:L.96 Salt bridges: D:K.74, D:K.74, D:K.74 pi-Stacking: D:H.92, D:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrique, L. et al., Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase. Nat Commun (2020)

Release Date

2020-07-15

Peptides

IMP-specific 5'-nucleotidase, putative: AC
IMP-specific 5'-nucleotidase, putative: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
D

D
D

IMP-specific 5'-nucleotidase, putative

IMP-specific 5'-nucleotidase, putative